There is humor in this.
Okay, let me qualify that. Case endlessly calls himself "meat." He has become quite jaded, and perhaps even humbled, by his awe-inspiring and addicting experiences in the Matrix. His mind works in mechanical ways, a habit stemming from his constant interface with technology, and his "missions" which require as much thinking on one's feet as they do planning. He is a cyborg right down to his synapses, as his very reflexes have been mechanically conditioned by his experiences in the matrix and on jobs. But every so often, he catches himself experiencing something human.
Ask yourself when the last time you caught yourself doing something human was, and you'll find yourself scratching your head; but Case notices the irony of his own situation.
This is one of the first indications that Case really does have a grip on the human element. I picture him saying this to himself, chuckling rather than grimacing. It amuses him to see everybody's -- and his own -- technological obsession while such basic human factors go ignored. Gibson didn't just toss this in randomly. "Why bother with the surgery... when you could just carry the thing around in your pocket" (14), Case says to himself. He laughs at "meat," but obviously respects it more than others realizing that meat is a defining human characteristic. His days as a "cowboy" (from "console cowboy") tell him that "cowboys didn't get into simstim because it was basically a meat toy" (55), but of course, he finds himself with simstim electrodes on his head; one of many examples of his recognition of human sense as being just as valid as simulated sense, or meat being just as valid as the wires attached to it.
...a tangible wave of longing hit him, lust and loneliness riding in on the wavelength of amphetamine. He remembered the smell of her skin in the overheated darkness of a coffin near the port, her fingers locked across the small of his back.
All the meat, he thought, and all it wants. (9)
He tortures his body, though. Jumping out of windows without apprehension is one thing, but sleeping in "coffins" is another. Coffins are matchbox-sized hotel rooms that consist of a bunk and nothing more. It dehumanizing to spend one's life traveling from coffin to coffin, as Case does. But he knows it. In reading "Case had rented a coffin here, on a weekly basis, since he'd arrived in Chiba, but he'd never slept in Cheap Hotel. He slept in cheaper places." (19), we see Gibson creating the vaguely amusing irony that gives a unique edge to Case's character.
We also see flashes of this irony in Molly, even early on, showing that she doesn't separate her mind from her body. "Nobody wants to hurt you," she says, "'Cept I do hurt people sometimes... I guess it's just the way I'm wired" (25). She knows what drives her, and it's not just her human instincts anymore. She laughs in disgust at this as much as Case does.
"Meat" gets referred to diminutively on the surface, but Gibson knows that it isn't just meat, and isn't just there to be defiled with gadgetry. Case recognized the beauty of the human body when "he lay on his side and watched [Molly] breathe, her breasts, the sweep of a flank defined with... elegance.... Her body was spare, neat, the muscles like a dancer's" (44).
So there is a twisted sort of ironic humor here after all, and in making fun of the body and passing it off as "meat," Gibson reminds us of what is most important and basic to us.